Genetic Diversity And Genome-wide Association Studies For Agronomic And Quality Traits Using SNP Markers In A Yangtze-huai Soybean Breeding Line Population

The achievements of crop breeding are largely depended on the discovery and utilization of elite parents,which including both core parents with high combining ability and superior comprehensive characters and donor parents with specific favorable gene(s).Thus,screening and creation of elite parents are one of the most important works in crop germplasm resource study.Molecular marker technology provides powerful tools for resolving genetic architecture of target traits and further for designing optimal hybrid crosses and marker-assisted selection.Yangtze-Huai valley and its northern region are important regions for soybean production in China and have abundant variety types such as spring and summer planting,harvest for grain,vegetable pod and other special use types.These genetic resources have great variation in characters and genetic basis,and new breeding lines could be obtained by extensive hybridization and recombination of these soybean materials.In this study,573 materails including breeding lines derived from the crosses between the four high quality core parents and many domestic or exotic germplasms and some parents were selected to establish a Yangtze-Huai soybean breeding line population(YHSBLP).Three qualitative traits(flower color,pubescence color and leaf shape)and eight agronomic and quality traits(lodging,plant height,main-stem node number,flower time,whole growth period,seed weight,protein content and oil content)were surveyed in 2013 and 2014.The genetic diversity and population structure of YHSBLP were analyzed by using SNP markers obtained through simplified genome re-sequencing technology(RAD-seq).Then,genome-wide association study(GWAS)was conducted by mixed linear model(MLM Q+K)approach in TASSEL V3.0 software,and elite alleles of some major associated loci for the agronomic and quality traits and their carriers were screened out.The main results were as follows:1.A set of high-quality genome-wide 61166 SNPs by RAD-seq was used in YHSBLP population,with most of 4844 SNPs on chromosome 18 and least of 1467 SNPs on chromosome 5.The average of gene diversity value was 0.31,ranged from 0.10?0.50.The materials in the population could be divided into three major groups according to cluster results of Neighbor-Joining analysis based on genetic distance.Most lines from the same cross were classified into the same cluster,and 54.83%of the pairwise kinship was less than 0.6.Total 3970 SNP markers were selected by using PLINK V1.07 to reveal the population structure by using ADMIXTURE V1.23 software,and it showed that the YHSBGP population was consisted of three subpopulations.All 61166 SNP markers were used to do principal component analysis by EIGENSOFT V5.0.1.The population could be classified into three subgroups based on the first two principal component factors.The LD decay in YHSBGP was about 1100 kb at r2=0.37 in YHSBLP population.2.In YHSBLP population,there were significant differences among the years,the soybean materials and the interaction between the soybean materials and the years in the eight agronomic and quality traits according to the results of analysis of variance.There were great phenotype variations and the heritability values were above of 72.96%.Association mapping was conducted to detect linked markers with QTL for the eight agronomic and quality traits and gene loci for three qualitative traits in the population based on MLM_Q+K model by TASSEL V3.0.A total of 2986 SNPs were identified to be significantly associated with eleven traits using significant level-log10P?3.The mapped regions of the genes for flower color,pubescence color and leaf shape were coincided with the previously reported positions,indicating the feasibility of using the population to do association mapping analysis.Total 489 SNPs for the eight quantitative traits could be detected across two years.Among them,there were 2,130 and 92 SNPs associated with lodging,plant height and main-stem node number respectively.A total of 58 and 23 SNPs associated with flower time and whole growth period were identified.There were 34 SNPs associated with seed weight.For seed protein and oil content,71 and 79 associated SNPs were found respectively.A total of 462 SNPs were identified to be significantly associated with eleven traits using significant level P?8.17×10-7(0.05/61166).The definition of QTLs was according to the distribution of the associated SNP markers.Among these QTLs,1 for lodging,20 for plant height,and 5 for main-stem node number were identified.Total 17 and 8 QTL for flower time and whole growth period were found respectively.13 QTL for seed weight,and 3 and 8 for seed protein and oil content were also obtained respectively.3.The allele effects of the SNP marker loci associated with agronomic and quality traits in two years were calculated,and some elite alleles with highest effects were selected.Among them,there were 12 positive and 8 negative alleles associated with plant height;2 positive and 3 negative alleles associated with main-stem node number;11 positive and 6 negative alleles associated with flower time;3 positive and 5 negative alleles associated with whole growth period;3 positive and 10 negative alleles associated with seed weight;5 positive alleles associated with oil content.Twenty specific lines with minimum or maximum values of each trait were selected to identify their allele composition.The information could be utilized in parent selection and cultivar development.In this study,it showed that there were great genetic variation of the agronomic and quality traits and SNP markers in Yangtze-Huai soybean breeding line population.The genetic structures of a number of elite lines were revealed by association mapping and elite alleles analysis,which could facilitate the further utilization of soybean breeding.